[BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml support

[Christian M Zmasek]

Hi:

> (BTW you will also notice that there is  
> nothing even close to the Swissprot "mnemonic" - nobody does this  
> except Swissprot - whose chief business is protein annotation, not  
> taxonomy - so you may want to consider how much significance you want  
> to give this in your object model.)
>   
Again, agreed. But in practice this  "mnemonic" is very, very useful. 
For example, it is a very handy way to create short protein 
names/identifiers which still contain human readable species information 
but are short enough the be used in a variety of alignment/phylogeny 
reconstruction programs.

> As an aside, the name of a taxon really is a proxy for a taxon  
> concept, whether that is a species or not, except that typically a  
> taxon name isn't given in full (i.e., with author, year, and  
> publication) to allow unambiguous identification. That's one of the  
> reasons why taxon identifiers are key.
Indeed.
And the taxon concept is a "science" in itself....

> BTW NCBI taxon IDs are just one  
> kind of taxon IDs. There are also Catalog of Life, ITIS, IPNI, and  
> others.
>   
Definitely. That's why the phyloxml taxonomy has a typed id.
Like so: <id type="ITIS">594569</id>.

--CZ